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101.
Phoebe J. Stewart‐Sinclair Kim S. Last Ben L. Payne Thomas A. Wilding 《Ecology and evolution》2020,10(7):3518-3534
Human‐induced climate change and ocean acidification (CC‐OA) is changing the physical and biological processes occurring within the marine environment, with poorly understood implications for marine life. Within the aquaculture sector, molluskan culture is a relatively benign method of producing a high‐quality, healthy, and sustainable protein source for the expanding human population. We modeled the vulnerability of global bivalve mariculture to impacts of CC‐OA over the period 2020–2100, under RCP8.5. Vulnerability, assessed at the national level, was dependent on CC‐OA‐related exposure, taxon‐specific sensitivity and adaptive capacity in the sector. Exposure risk increased over time from 2020 to 2100, with ten nations predicted to experience very high exposure to CC‐OA in at least one decade during the period 2020–2100. Predicted high sensitivity in developing countries resulted, primarily, from the cultivation of species that have a narrow habitat tolerance, while in some European nations (France, Ireland, Italy, Portugal, and Spain) high sensitivity was attributable to the relatively high economic value of the shellfish production sector. Predicted adaptive capacity was low in developing countries primarily due to governance issues, while in some developed countries (Denmark, Germany, Iceland, Netherlands, Sweden, and the United Kingdom) it was linked to limited species diversity in the sector. Developing and least developed nations (n = 15) were predicted to have the highest overall vulnerability. Across all nations, 2060 was identified as a tipping point where predicted CC‐OA will be associated with the greatest challenge to shellfish production. However, rapid declines in mollusk production are predicted to occur in the next decade for some nations, notably North Korea. Shellfish culture offers human society a low‐impact source of sustainable protein. This research highlights, on a global scale, the likely extent and nature of the CC‐OA‐related threat to shellfish culture and this sector enabling early‐stage adaption and mitigation. 相似文献
102.
Henderson R Chen S Chen JZ Grigorieff N Passmore LA Ciccarelli L Rubinstein JL Crowther RA Stewart PL Rosenthal PB 《Journal of molecular biology》2011,413(5):1028-1046
The comparison of a pair of electron microscope images recorded at different specimen tilt angles provides a powerful approach for evaluating the quality of images, image-processing procedures, or three-dimensional structures. Here, we analyze tilt-pair images recorded from a range of specimens with different symmetries and molecular masses and show how the analysis can produce valuable information not easily obtained otherwise. We show that the accuracy of orientation determination of individual single particles depends on molecular mass, as expected theoretically since the information in each particle image increases with molecular mass. The angular uncertainty is less than 1° for particles of high molecular mass (∼ 50 MDa), several degrees for particles in the range 1-5 MDa, and tens of degrees for particles below 1 MDa. Orientational uncertainty may be the major contributor to the effective temperature factor (B-factor) describing contrast loss and therefore the maximum resolution of a structure determination. We also made two unexpected observations. Single particles that are known to be flexible showed a wider spread in orientation accuracy, and the orientations of the largest particles examined changed by several degrees during typical low-dose exposures. Smaller particles presumably also reorient during the exposure; hence, specimen movement is a second major factor that limits resolution. Tilt pairs thus enable assessment of orientation accuracy, map quality, specimen motion, and conformational heterogeneity. A convincing tilt-pair parameter plot, where 60% of the particles show a single cluster around the expected tilt axis and tilt angle, provides confidence in a structure determined using electron cryomicroscopy. 相似文献
103.
The genome of the Lyme disease-causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated proteins - Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb-DNA complex in which the DNA is bent by over 180 degrees . We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout. 相似文献
104.
When searching for their favorite host tissues, animal viruses frequently attach to cell-surface receptors that have key roles in normal cell physiology. Integrins are prime examples of physiologically important receptors that have been usurped by nonenveloped and enveloped viruses for attachment and/or cell entry. This family of heterodimeric receptors mediates cell adhesion, cell migration, tumor metastasis and cell differentiation. Recent investigations have shed new light on integrin structure as well as on the underlying molecular features of their association with viral ligands. In this review, we discuss several examples of virus-integrin interactions that highlight recent advances in this field. The continuing improvements in virus and cell imaging techniques have helped to uncover the molecular basis of how integrins are recognized by such a wide range of microbial pathogens to invade host cells. 相似文献
105.
Yvonne C. Collingham Brian Huntley Res Altwegg Phoebe Barnard Oliver S. Beveridge Richard D. Gregory Lucy R. Mason H. Dieter Oschadleus Robert E. Simmons Stephen G. Willis Rhys E. Green 《Ibis》2014,156(4):741-754
Estimates of annual survival rates of birds are valuable in a wide range of studies of population ecology and conservation. These include modelling studies to assess the impacts of climatic change or anthropogenic mortality for many species for which no reliable direct estimates of survival are available. We evaluate the performance of regression models in predicting adult survival rates of birds from values of demographic and ecological covariates available from textbooks and databases. We estimated adult survival for 67 species using dead recoveries of birds ringed in southern Africa and fitted regression models using five covariates: mean clutch size, mean body mass, mean age at first breeding, diet and migratory tendency. Models including these explanatory variables performed well in predicting adult survival in this set of species, both when phylogenetic relatedness of the species was taken into account using phylogenetic generalized least squares (51% of variation in logit survival explained) and when it was not (48%). Two independent validation tests also indicated good predictive power, as indicated by high correlations of observed with expected values in a leave‐one‐out cross validation test performed using data from the 67 species (35% of variation in logit survival explained), and when annual survival rates from independent mark–recapture studies of 38 southern African species were predicted from covariates and the regression using dead recoveries (48%). Clutch size and body mass were the most influential covariates, both with and without the inclusion of phylogenetic effects, and a regression model including only these two variables performed well in both of the validation tests (39 and 48% of variation in logit survival explained). Our regression models, including the version with only clutch size and body mass, are likely to perform well in predicting adult survival rate for southern African species for which direct survival estimates are not available. 相似文献
106.
107.
Helianthous Verma Roshan Kumar Phoebe Oldach Naseer Sangwan Jitendra P Khurana Jack A Gilbert Rup Lal 《BMC genomics》2014,15(1)
Background
Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Here, we examined the evolution and diversification of the lin pathway under the selective pressure of HCH, by comparing the draft genomes of six newly-sequenced Sphingobium spp. (strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH dumpsites, with three existing genomes (S. indicum B90A, S. japonicum UT26S and Sphingobium sp. SYK6).Results
Efficient HCH degraders phylogenetically clustered in a closely related group comprising of UT26S, B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies with ANI value >98%. Less than 10% of the total gene content was shared among all nine strains, but among the eight HCH-associated strains, that is all except SYK6, the shared gene content jumped to nearly 25%. Genes associated with nitrogen stress response and two-component systems were found to be enriched. The strains also housed many xenobiotic degradation pathways other than HCH, despite the absence of these xenobiotics from isolation sources. Additionally, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, LL03, P25 and RL3 were identified as lin deficient strains, as they housed incomplete lin pathways. Further, in HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and linA2 known for their different enantioselectivity.Conclusion
The bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users. 相似文献108.
Wing Chee So Terence Han-Wei Ching Phoebe Elizabeth Lim Xiaoqin Cheng Kit Yee Ip 《PloS one》2014,9(11)
The present study investigates whether producing gestures would facilitate route learning in a navigation task and whether its facilitation effect is comparable to that of hand movements that leave physical visible traces. In two experiments, we focused on gestures produced without accompanying speech, i.e., co-thought gestures (e.g., an index finger traces the spatial sequence of a route in the air). Adult participants were asked to study routes shown in four diagrams, one at a time. Participants reproduced the routes (verbally in Experiment 1 and non-verbally in Experiment 2) without rehearsal or after rehearsal by mentally simulating the route, by drawing it, or by gesturing (either in the air or on paper). Participants who moved their hands (either in the form of gestures or drawing) recalled better than those who mentally simulated the routes and those who did not rehearse, suggesting that hand movements produced during rehearsal facilitate route learning. Interestingly, participants who gestured the routes in the air or on paper recalled better than those who drew them on paper in both experiments, suggesting that the facilitation effect of co-thought gesture holds for both verbal and nonverbal recall modalities. It is possibly because, co-thought gesture, as a kind of representational action, consolidates spatial sequence better than drawing and thus exerting more powerful influence on spatial representation. 相似文献
109.
The effects of insects,nutrients, and plant invasion on community structure and function above‐ and belowground 下载免费PDF全文
Phoebe Wright Melissa A. Cregger Lara Souza Nathan J. Sanders Aimée T. Classen 《Ecology and evolution》2014,4(6):732-742
Soil nutrient availability, invasive plants, and insect presence can directly alter ecosystem structure and function, but less is known about how these factors may interact. In this 6‐year study in an old‐field ecosystem, we manipulated insect abundance (reduced and control), the propagule pressure of an invasive nitrogen‐fixing plant (propagules added and control), and soil nutrient availability (nitrogen added, nitrogen reduced and control) in a fully crossed, completely randomized plot design. We found that nutrient amendment and, occasionally, insect abundance interacted with the propagule pressure of an invasive plant to alter above‐ and belowground structure and function at our site. Not surprisingly, nutrient amendment had a direct effect on aboveground biomass and soil nutrient mineralization. The introduction of invasive nitrogen‐fixing plant propagules interacted with nutrient amendment and insect presence to alter soil bacterial abundance and the activity of the microbial community. While the larger‐scale, longer‐term bulk measurements such as biomass production and nutrient mineralization responded to the direct effects of our treatments, the shorter‐term and dynamic microbial communities tended to respond to interactions among our treatments. Our results indicate that soil nutrients, invasive plants, and insect herbivores determine both above‐ and belowground responses, but whether such effects are independent versus interdependent varies with scale. 相似文献
110.